Well, they're just colors (RGB in hex) so if you do something goofy the worst that will happen is your bootup flubber animation will look like someone barfed on it.
These are three color components that are used in the startup animation, between the "X2 config live loading" and the Xbox "Xecuter rox my box!" screens. If memory serves they had previously only been one colorFlubberScene option in the earlier X2CL versions, the more recent broke it out into more granular components. From the ambient, diffuse and specular comments these must be lighting color controls. I haven't played around with them myself so I don't know how altering each one will change the look of the animation.
To learn more about them you'll need to do the same thing I may do in a bit, expiriment with them. As I said they're just color controls, changing these will not FRAG your box. (... he says confidently, setting himself up for trouble.)
-Whoopin'